To set up lircd with the hdhomerun to see a tivo series 2 remote control, you should first program the HDHomeRun to send UDP packets to your linux computer with a command such as the following:
hdhomerun_config <device id> set /ir/target "<lircd ip addr>:<port> store"
You can test that this is working by running:
irrecord -H udp -d 5000 "testing"
If you get dots when you press your remote control buttons, the HDHomeRun is sending IR information to your linux box. (remember to unblock UDP port 5000 for incoming transmissions if you are running a firewall!)
Once that is working, just set up your /etc/lirc hardware.conf and lircd.conf files to support the Tivo series 2 remote.